bridge-rna

Imported from de-jish/bridge-rna (AGENTS.md). Install upstream with npx skills add de-jish/bridge-rna. Copyright stays with the author.

Bridge RNA contributor guidance

Read CLAUDE.md for architecture, scientific invariants, commands, and the existing visual language.

Interface copy and feature simplicity

• Before planning, implementing, or reviewing any UI or UX change, load and use both taste (design-taste-frontend) and impeccable. This applies to every agent. Report a missing skill explicitly. Apply both again during final review.
• Preserve the navy header, teal rule, existing type, accessible tokens, and data encodings. Refine the working instrument rather than redesigning it.
• Write plain, precise copy. Name actions and their objects consistently. Avoid promotional claims, repeated instructions, decorative badges, and authored em dashes. Preserve punctuation in scientific notation and source metadata.
• Describe the actual reference collection and query source. Embedding cosine similarity does not establish biological equivalence; projected map distances do not determine retrieval rank.
• Distinguish source annotations from derived tissue categories and AI interpretation. Keep identifiers, source links, provenance, missing-data distinctions, and reproduction settings accessible.
• Give each action one clear entry point. Do not expose graph selection tools without a consumer for the selection. Prefer inline counts over standalone statistic cards; when a diagnostic feature is explicitly retired, remove its UI, callback, payload, and orphan styles while preserving independently used scientific validation.
• Use contextual disclosures for secondary explanations and specialized settings. Remove a capability only after tracing its dependencies and establishing redundancy or lack of research value. Do not call it unused without usage evidence.
• Keep sample identities, metadata, labels, and coordinates aligned. A cosmetic cleanup must not change preprocessing, embeddings, ranking, grouping, or projection algorithms. Document scientific concerns separately.
• Verify representative sample, cohort, upload, map, metadata, and available export workflows in the running app. Check desktop and narrow layouts, review the scientific diff, and preserve unrelated work when committing.

Prefer rtk-prefixed shell commands when installed. If it is unavailable, report that and use a transparent command fallback.

NASA shipping boundary

When asked to ship changes, follow docs/deployment.md and use deploy/ship.py. Use only SFTP/SCP file operations within /home/ubuntu/fm_viz_new via the existing nasa-server alias. Never execute remote shell commands, helpers, installers or process controls; never access the earlier deployment outside this directory. Do not download secrets, private configuration or uploads, or follow remote symlinks. Review source/server diffs, validate locally, back up permitted code and transfer only into .ship/incoming/ID. The user runs apply and Gunicorn. Transferred and confirmed running are separate states.